First, follow Carl... up the stairs and to the light. On the way you'll pass by a handle from a gate that is infested with spiders, remember its location, because you'll have to come back here.
Once you get out of the jungle, you'll reach ruins where two large dinosaurs are going to roam around. Squat and slowly move up near them to a safe place in the ruins (behind the pillars - Carl will go there and will show you the way).
There you'll find worms which I'll show you how to use in a very useful way. Tamp one onto the spear and go with it to the higher part of the building using the stairs.
Hurl it to the spot where the orange arrow points at, in the grass. It'll make the dinosaurs suddenly go there (blue arrow), then, shoot the container with fire with pistol (red arrow). This way you'll kill both at once :), without using much ammo.
The flying creature that cruises around there might still be a small problem. Once the dinosaurs are dead, he'll go and eat them (his location is pointed out on the right picture, on the column). Once he's eating, throw bones at him, after a couple of throws he'll die (he shouldn't attack you).
Now when the danger is gone, look for the handles needed to open the gate. The first one is located behind the bushes, inside the ruins (to the left of the gate - left picture). Light up the bushes and take it. The second one is guarded by spiders (the location you were supposed to remember), draw them off of it with a spider tamped on a spear and safely take the handle.
Before ending this stage, don't forget about the ammunition in the crate (near the spot that you hid in the beginning).
Another portion of ammo is waiting for you behind the gate, in a destroyed building. Choose which gun you prefer, shotgun or pistol (I advise the pistol, you'll have a lot more ammo).
Once you move on, you'll reach a spot where you'll be outside again once you go through a hole in the wall. Right after going through it you'll be attacked by one worm (the creepy one - two shots and it's dead).
From there, jump to a larger cave through the waterfall. At the bottom you'll be attacked by two worms, and when you'll be moving on with the current of the water, every once in a while another worm will attack you. Kill every one of with the pistol.
Once you reach the place where you'll be able to get out of the river, go through a long tunnel in which a creature will attack you.
Then, you'll reach a huge, broad cave and you'll meet one of the crew members, dark skinned Hayes, on the other side of the scarp.
To get to him, you first have to turn left and walk through the water (there will be fish in it, tamp one onto the spear, it will be useful later on as a decoy). Once you've reach the place where you'll get out onto land, very quickly run to the tunnel in front of you (right picture). There are two large dinosaurs roaming around, which can easily kill you.
From there, run to the next cover (second one), and then to the third cover (right picture).
Now, go into the tunnel near a wall of a huge cave (left picture), and once there, run under an arch in the wall (right picture - you can use the fish in this spot, since the distance is a little bigger than in other cases). There, jump into the water. You can feel safe for a moment.
Swim through the 'pool' and walk up the stairs onto a higher level.
You'll stand in front of Hayes who's going to be attacked. Hurl a spear at the creature (they lie nearby) or shoot it if you won't have enough time for the spear. The dinosaur will then jump over to you and you'll have to defend. Fill him up with lead until he dies (he's the stronger one, so he'll take a lot). Also, tell Hayes to give you his weapon (he'll throw it over), it's a machine gun with which you'll eliminate opponents prowling between hideouts through which you just came in.
Light up a spear and unblock a path for Hayes, by throwing it into the bushes near the spot you came in (to the left of the waterfall). Thanks to this, the crew will be reunited again.
After that, go back to the dinosaurs you evaded earlier (two) and kill them using the new weapon.
Once you're done with that, at the end of one of the tunnels there will be a tilted pole with a handle needed to open a gate. Take it and place it where you need it (the gate is located near the last hideout).
When you'll be going through it, you'll pass a small hall, from which you'll get to an underground stream. By following the stream (nothing will attack you anymore in this stage), you'll reach a broad lake and hear a roar and human screams far away.
Swim on further, until you get onto land again, get out of the cave and go to the fortress.